Changing the W-2 as you describe means that your copy of the W-2 will not match the copy that was sent to the IRS. This is likely to generate a letter from the IRS assessing you extra tax, and asking you to explain what you did.
That's why I would encourage you to read this IRS page all the way to the bottom. because it describes the steps you should take in your situation.
If you have a IRS Taxpayer Assistance Center near you, that would be a great help. But, the final result is that you will likely complete a 4852 and add it to your return, as Diane said.
What you must do is document everything, especially how you know that the FSA contributions were removed from your Wages, which is clear evidence that your employer just made a mistake in box 10 of your W-2.
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